Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
MC JC	NZ_CP009273	2,399,465	Δ7 bp	coding (650‑656/939 nt)	lrhA ←	transcriptional regulator LrhA

Missing coverage evidence...
			seq id	start	end	size	←reads	reads→	gene	description
*	*	÷	NZ_CP009273	2399465	2399471	7	21 [0]	[0] 21	lrhA	transcriptional regulator LrhA

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NZ_CP009273	= 2399464	0 (0.000)	21 (0.970)	13/164	0.4	100%	coding (657/939 nt)	lrhA	transcriptional regulator LrhA
	?	NZ_CP009273	2399472 =	0 (0.000)					coding (649/939 nt)	lrhA	transcriptional regulator LrhA

CTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGGCGACATAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGC  >  NZ_CP009273/2399390‑2399548                                                                                   |                                                                             gtccgggctcatcatctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggcgggaagcgtcgagAAGCCAGt                                                                       <  1:366903‑M2/8‑1 (MQ=255)          catcatctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGa                                                              >  1:191160‑M2/74‑90 (MQ=255)          catcatctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGa                                                              >  1:222385‑M2/74‑90 (MQ=255)                ctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCa                                                                         >  1:112552‑M2/68‑73 (MQ=255)                ctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCa                                                                         <  2:112552‑M2/6‑1 (MQ=255)                        gcctcgccgccacgccaagaccggctttcactgccgcacgaacggcccgaagcttcgagAAGCCAGTCGCCATGGAATATCTGCTttatt                                                <  2:399299‑M2/31‑1 (MQ=255)                             gccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCg                                           <  1:224896‑M2/36‑1 (MQ=255)                                  cacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGcc                                      >  1:231401‑M2/50‑90 (MQ=255)                                              ggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATc                                                         <  1:548784‑M2/22‑1 (MQ=255)                                              ggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATc                                                         >  2:548784‑M2/38‑59 (MQ=255)                                                    cactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAAc                    <  2:74462‑M2/59‑1 (MQ=255)                                                    cactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAAc                    <  2:531286‑M2/59‑1 (MQ=255)                                                    cactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAAc                    <  2:271612‑M2/59‑1 (MQ=255)                                                    cactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAAc                    <  2:240345‑M2/59‑1 (MQ=255)                                                    cactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAAc                    <  2:222385‑M2/59‑1 (MQ=255)                                                    cactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAAc                    <  1:81438‑M2/59‑1 (MQ=255)                                                     actgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACg                   <  2:283801‑M2/60‑1 (MQ=255)                                                        gccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACg                   >  2:312420‑M2/28‑87 (MQ=255)                                                        gccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACg                   <  1:312420‑M2/60‑1 (MQ=255)                                                                      cggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGc  <  2:272284‑M2/77‑1 (MQ=255)                                                                      cggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGc  <  2:191160‑M2/77‑1 (MQ=255)                                                                                   |                                                                             CTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGGCGACATAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGC  >  NZ_CP009273/2399390‑2399548

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑
Reads not counted as support for junction
read_name Not counted due to insufficient overlap past the breakpoint.
read_name Not counted due to not crossing MOB target site duplication.